[Bioc-devel] Tips for using R-2.15 with BioC 2.10 and 2.11

[Kasper Daniel Hansen]

Robert,

I have not tried the new setup yet, but I doubt you want to put it in
.bash_profile.  I would use .profile or .bashrc.  Furthermore, note
that this will not work if you use the GUI, as the GUI is not affected
by the .profile/.bash_profile/.bashrc.

Kasper

On Tue, Apr 17, 2012 at 9:50 AM, Steve Lianoglou
<mailinglist.honeypot at gmail.com> wrote:
> FWIW, I have a very similar (but much more kindergarden like) script
> as Nico. So far I think it's working out OK, although I don't hop
> around between devel and release too often, I have once or twice.
>
> -steve
>
>
> On Tue, Apr 17, 2012 at 9:12 AM, Nicolas Delhomme <delhomme at embl.de> wrote:
>> Dear Robert,
>>
>> I have made myself a small shell script that sets the environment variable R_LIBS and then start R.:
>>
>> #!/bin/bash
>>
>> ## the profile
>> export R_PROFILE=/Users/delhomme/etc/R-profile-for-R-2.16.site
>>
>> ## the R libs
>> if test -z $R_LIBS
>>     then
>>    export R_LIBS=/Users/delhomme/opt/R-libs-for-R-2.16
>> else
>>     export R_LIBS=$R_LIBS:/Users/delhomme/opt/R-libs-for-R-2.16
>> fi
>> echo $R_LIBS
>>
>> ## start R
>> exec /Users/delhomme/opt/R-2.16.0/bin/R $@
>>
>> HTH,
>>
>> Nico
>>
>> ---------------------------------------------------------------
>> Nicolas Delhomme
>>
>> Genome Biology Computational Support
>>
>> European Molecular Biology Laboratory
>>
>> Tel: +49 6221 387 8310
>> Email: nicolas.delhomme at embl.de
>> Meyerhofstrasse 1 - Postfach 10.2209
>> 69102 Heidelberg, Germany
>> ---------------------------------------------------------------
>>
>>
>>
>>
>>
>> On 17 Apr 2012, at 15:00, Robert Castelo wrote:
>>
>>> Dear Dan, and specially those using mac osx for developing packages,
>>>
>>> i've tried to follow the instructions below for Mac OSX, concretely
>>>
>>> On 04/03/2012 01:04 AM, Dan Tenenbaum wrote:
>>>> Hello BioC Developers,
>>>>
>>> [...]
>>>
>>>> On Linux and Mac OS X, You can create bash aliases (called e.g. Rdevel
>>>> and Rrelease) that will invoke the command line above. (Note that the
>>>> "devel" in "Rdevel" refers not to the development version of R, but to
>>>> that of Bioconductor; slightly confusing). Put the following in
>>>> ~/.bash_profile:
>>>>
>>>> # Mac OS X
>>>> alias Rdevel='R_LIBS_USER=~/Library/R/2.15-bioc-devel/library R'
>>>> alias Rrelease='R_LIBS_USER=~/Library/R/2.15-bioc-release/library R'
>>>
>>> i've created this ~/.bash_profile in my laptop running Mac OSX 10.6.8 and when i start with
>>>
>>> $ Rdevel
>>>
>>> my .libPaths() always reports the release directory and never the devel directory, i.e.,
>>>
>>> > .libPaths()
>>> [1] "/Users/rcastelo/Library/R/2.15-bioc-release/library"
>>> [2] "/Library/Frameworks/R.framework/Versions/2.15/Resources/library"
>>>
>>> if i rename '~/Library/R/2.15-bioc-release' to 'tmp' or i comment the alias line about the release in the .bash_profile (i.e., trying to force the system to see only ~/Library/R/2.15-bioc-devel/library) i only get the default path, i.e.,
>>>
>>> > .libPaths()
>>> [1] "/Library/Frameworks/R.framework/Versions/2.15/Resources/library"
>>>
>>> i've checked permissions and both directories ~/Library/R/2.15-bioc-release/library and ~/Library/R/2.15-bioc-devel/library are exactly the same in this regard (drwxr-xr-x).
>>>
>>> can any Mac OSX user replicate this problem?
>>>
>>> if not, i guess i must be doing something wrong, but i have no clue what it could be, any hint to a possible diagnostic/QC will be very much appreciated.
>>>
>>> thanks,
>>> robert.
>>>
>>> _______________________________________________
>>> Bioc-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
>
> --
> Steve Lianoglou
> Graduate Student: Computational Systems Biology
>  | Memorial Sloan-Kettering Cancer Center
>  | Weill Medical College of Cornell University
> Contact Info: http://cbio.mskcc.org/~lianos/contact
>
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